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ChAMP
•
reset
6
votes
2
replies
5.6k
views
What is logFC and "B" in methylation analysis ??
limma
champ
logfc
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
AST
▴ 60
4
votes
4
replies
2.9k
views
How to remove unwanted probes before normalization in 450k data
minfi
450k
champ
rnbeads
updated 8.1 years ago by
James W. MacDonald
65k • written 8.1 years ago by
AST
▴ 60
3
votes
9
replies
3.7k
views
champ.runCombat is failing: "invalid 'row.names' length"
champ
5.7 years ago
Gurkenkönig
▴ 10
3
votes
6
replies
2.0k
views
could not find function "champ.load"
ChAMP
champ 2.9.10
methylationepic
6.1 years ago
david.ch
• 0
3
votes
5
replies
2.1k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation
ChAMP
updated 8 weeks ago by
sup0903
• 0 • written 3.4 years ago by
Hongbii
• 0
3
votes
7
replies
5.4k
views
error with champ.load
champ
written 6.5 years ago by
o.giannakopoulou
▴ 10
3
votes
4
replies
3.0k
views
Error while using champ.svd() function in subset of data
ChAMP
methylationepic
epicarray
epigenomics
updated 6.6 years ago by
rcavalca
▴ 140 • written 6.6 years ago by
karthikrpad
▴ 10
3
votes
4
replies
8.6k
views
Problem loading R packages on MacBook Pro
newpackage
ChAMP
updated 19 months ago by
Yi Ping
• 0 • written 2.4 years ago by
Brendon
• 0
2
votes
1
reply
562
views
ChAMP can't be found in Bioc3.18?
ChAMP
5 months ago
ramonfallon
▴ 20
2
votes
1
reply
1.2k
views
How to download the ChAMP dependency ChAMPdata
ChAMP
ChAMPdata
updated 3.0 years ago by
shepherl
3.8k • written 3.0 years ago by
Federica
▴ 10
2
votes
2
replies
1.2k
views
Champ.lasso error @ dmr.beta.means[,22:24]
ChAMP
updated 8.2 years ago by
david.watson
▴ 30 • written 8.8 years ago by
zhourudy2
▴ 10
2
votes
3
replies
1.6k
views
champ.impute doesn't update beta matrix
champ
impute
bioconductor
updated 7.1 years ago by
Yuan Tian
▴ 90 • written 7.1 years ago by
rasmus.rydbirk
▴ 10
2
votes
16
replies
2.5k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation
epic
champ
champ.load()
Methylation array
updated 4.3 years ago by
Yuan Tian
▴ 280 • written 4.3 years ago by
Ankit
▴ 20
2
votes
1
reply
1.0k
views
How to save results of each step from ChAMP pipeline?
Bioconductor
ChAMP
updated 2.9 years ago by
Yuan Tian
▴ 280 • written 2.9 years ago by
Federica
▴ 10
2
votes
4
replies
1.4k
views
bumphunter stalls on "Smoothing coefficients"
bumphunter
ChAMP
updated 4.9 years ago by
Yuan Tian
▴ 280 • written 4.9 years ago by
rasmus.rydbirk
▴ 10
2
votes
1
reply
1.3k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation
epic
champ
updated 5.4 years ago by
Yuan Tian
▴ 280 • written 5.4 years ago by
D
▴ 10
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 20 days ago by
Tim Peters
▴ 170 • written 5 months ago by
rae.alshammari
▴ 10
2
votes
7
replies
2.4k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 6 months ago by
dorota.komar
• 0 • written 3.4 years ago by
Ankit
▴ 20
2
votes
3
replies
1.7k
views
ChAMP was installed and library in R, however, I can't use the function
champ
6.1 years ago
doctorjiangtao
▴ 10
2
votes
3
replies
2.2k
views
Error in champ.load (v. 2.8.3)
champ
ChAMP
updated 6.8 years ago by
Yuan Tian
▴ 90 • written 6.8 years ago by
rasmus.rydbirk
▴ 10
2
votes
3
replies
2.1k
views
"Seems your IDAT file not from one Array"
EPIC
methylation
ChAMP
updated 6.0 years ago by
yura.grabovska
▴ 30 • written 6.1 years ago by
david.ch
• 0
2
votes
5
replies
2.3k
views
DMRcate fails in ChAMP package
ChAMP
updated 7.1 years ago by
Yuan Tian
▴ 90 • written 7.1 years ago by
rasmus.rydbirk
▴ 10
2
votes
5
replies
1.8k
views
Error in Champ for Bioconductor performing GSEA analysis on Methlayion array data
champ
bioconductor
methyaltion
epic array
updated 5.2 years ago by
godai987654
• 0 • written 5.3 years ago by
erinkello
• 0
2
votes
5
replies
1.9k
views
Problem at champ.load
ChAMPdata
ChAMP
updated 5 weeks ago by
James W. MacDonald
65k • written 12 months ago by
angel
• 0
1
vote
16
replies
3.2k
views
error in ChAMP loading file
ChAMP
updated 5 weeks ago by
hortense96
• 0 • written 17 months ago by
Giulia
• 0
1
vote
2
replies
2.5k
views
Error using ChAMP SVD analysis
ChAMP
updated 13 months ago by
Seohyun
• 0 • written 2.8 years ago by
FWNL15
• 0
1
vote
0
replies
1.3k
views
How to find DMRs using probe-lasso from ChAMP using minfi data
ChAMP
minfi
DMR
dmr analysis
lasso
8.5 years ago
AST
▴ 60
1
vote
1
reply
1.3k
views
ChAMP probe.features displays only CHR and MAPINFO, and it entails epic data, whereas probe.features.epic does not exist
champ
7.9 years ago
line.heylen
▴ 10
1
vote
1
reply
1.4k
views
Error in champ.lasso of ChAMP Bioconductor package for Methylation 450k analysis
ChAMP
8.8 years ago
junyupub
• 0
1
vote
1
reply
263
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray
methylationArrayAnalysis
ChAMP
updated 8 weeks ago by
James W. MacDonald
65k • written 8 weeks ago by
david.cheishvili
• 0
1
vote
2
replies
1.4k
views
Problem installing ChAMP package.
software error
microarray
champ
methylation
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
cawten
▴ 10
1
vote
2
replies
117
views
Error in champ.load(): The following specified files do not exist
ChAMP
5 days ago • updated 4 days ago
Sherin
• 0
1
vote
4
replies
2.4k
views
New version of ChAMP can not proceed through champ.DMP
champ
6.7 years ago
sarka.vorackova
• 0
1
vote
1
reply
1.3k
views
How to solve the error in running champ.DMP()
ChAMP
updated 2.9 years ago by
Basti
▴ 770 • written 2.9 years ago by
Federica
▴ 10
1
vote
4
replies
106
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 14 hours ago by
James W. MacDonald
65k • written 4 days ago by
Mirella Aurora
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 5 days ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
1
vote
3
replies
2.7k
views
normalization combination of noob + BMIQ/Quantile
minfi
bmiq
noob
preprocessQuantile
champ
updated 3.6 years ago by
James W. MacDonald
65k • written 3.6 years ago by
Lin
▴ 50
1
vote
1
reply
810
views
Issue with ChAMP DMP.GUI
ChAMP
champ
methylation
EPIC
updated 4.3 years ago by
Yuan Tian
▴ 90 • written 4.3 years ago by
cherlyn.t
• 0
1
vote
3
replies
1.3k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
4.2 years ago
erwin.tomasich
▴ 10
1
vote
2
replies
1.1k
views
ChAMP not handling 3+ levels in contrasts
champ
updated 4.6 years ago by
Yuan Tian
▴ 280 • written 4.6 years ago by
ognjen011
• 0
1
vote
2
replies
1.9k
views
Manhattan plot from ChAMP data
champ
plot
manhattan plot
updated 7.1 years ago by
Yuan Tian
▴ 90 • written 7.1 years ago by
rasmus.rydbirk
▴ 10
1
vote
2
replies
1.1k
views
what is "sample_well" and "pool_ID" in ChAMP
ChAMP
3.4 years ago
Hongbii
• 0
1
vote
1
reply
1.2k
views
Batch Correction and Normalization for champ.CNA
bioconductor
ChAMP
copy number
batch effect
normalization
updated 7.1 years ago by
rasmus.rydbirk
▴ 10 • written 7.1 years ago by
apmishra
• 0
1
vote
5
replies
2.2k
views
error while using champ.svd() function
champ
5.3 years ago
sinha.puja
▴ 10
1
vote
3
replies
1.5k
views
Error biocLite() newest version of ChAMP
R
bioclite
champ
6.0 years ago
rosa_hegi
▴ 10
1
vote
1
reply
823
views
champ.DMP finds different probes in A-vs-B and B-vs-A analysis
DifferentialMethylation
ChAMP
champ.DMP
updated 3.4 years ago by
Yuan Tian
▴ 280 • written 3.4 years ago by
Ricardo
• 0
1
vote
8
replies
2.7k
views
Error in Champ for Bioconductor analyzing Methlayion array data
champ
bioconductor
contrastmatrix
compare.group
updated 5.3 years ago by
Yuan Tian
▴ 280 • written 5.3 years ago by
erinkello
• 0
1
vote
1
reply
1.1k
views
How to suggest BiocViews tags for an existing package?
biocviews
champ
8.6 years ago
Peter Hickey
▴ 740
1
vote
3
replies
2.1k
views
champ.DMP phenotypes and covariates
champ
champ.dmp()
updated 6.5 years ago by
Yuan Tian
▴ 280 • written 6.5 years ago by
o.giannakopoulou
▴ 10
1
vote
2
replies
2.3k
views
Beta-matrix - Differential methylation analysis
ChAMP
tutorial
6.0 years ago
Dave Emir
• 0
50 results • Page
1 of 1
Recent ...
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Comment: DESeq2 - dispersion estimation when there is none
by
WardDeb
• 0
Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
Gayatri
• 0
Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
Answer: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
Tim Peters
▴ 170
Hi Jose and Russ, Apologies to Jose for not seeing this earlier. Sometimes the loess smoother in the bottom panel will throw this error …
Comment: Trying to use enrichGO
by
fernanda.backsouza
• 0
Sure, I changed it but still NULL G0 <- enrichGO( gene = ortologos_filtrados$Gene.ID, OrgDb = org.Cs.eg.db, keyType = "ENTREZID",…
Answer: limma-voom: Calculate the log-fold change in gene expression within a sample
by
Gordon Smyth
50k
No, you cannot use residuals to compute logFCs. From the information you give, I guess that you need to add individual-specific condition …
Votes
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
Answer: Differentially expressed genes in monocle pseudotime
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